We recently installed two separate risers covering several different areas of the building. Each is covered by its own FDC located on the same side of the building.

The fire marshal recently commented that the two fire systems have to be connected together, With one FDC. Is this an NFPA code requirement or other national code requirement?

The last civil design we did the fire marshal made us use only one FDC.  I don't believe this was a code requirement, just the personal preference of the fire marshal.  Their rationale was that they didn't want the firefighters looking around for different FDC's or worrying about whether they were hooked up to the right FDC.  This was for a 100,000 square foot one story building.

I have done something similar on many large warehouse projects.  There is a supply from the city main to the pump room.  From there, we exit the pump and install the underground fire loop around the building.  This puts all of the hydrants on the loop at pump pressure.  We then installed 2-way hydrants, instead of the 3-way with pumper connections.  The AHJ ws just concerned that some one would try to connect from the pumper outlet on the hydrant to the pump on the truck.  Since the hydrants only had 2.5" outlets, that was not a problem.  

The only thing that would caution me in your scenario is if the hydrants are not on a dedicated fire line.  You don't want to charge the water loop if there are domestic devices coming off of it.  In the situation I described above, we always had a dedicated fire loop around the building.

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